I'm a little confused on how the whole application process works. I heard that its ok to submit your PGRE scores after the deadline. But, for example on the Columbia Applied physics and math program, it says

"Can I submit my application first and send supplemental material later when available? You may submit the online application first and send test scores or recommendation letters after if necessary and prior to the deadline. All other supplemental material must be submitted together with the online application.

Be advised that after the deadline to apply Columbia reserves the right to evaluate an application and render a final decision even if all pieces of the application have not been received. Furthermore, once the application is under evaluation it can not be updated to include new supplemental material received and may be considered for admission as is.

Where do I mail official transcripts? Copies of your transcripts should be uploaded online and the official transcript sealed by the institution mailed to the Office.."

I'm confused. So I just upload UNOFFICIAL copies of my transcript, and submit it at the same time as my application? it doesnt say anything if those copies can be unofficial, but that has to be the case since its impossible to upload my official one. Then, its still ok to submit the OFFICIAL transcript AFTER i submit the online application? or is there a chance that they could evaluate it before they receive my OFFICIAL transcripts? Is this normal for other grad programs?

The reason they allow your official scores and transcripts to come in later is because those are somewhat out of your control. Typically your school has to mail the transcript, and the scores are at the mercy of the ETS. The November scores also might not be ready in time for some application deadlines. You won't get rejected because your official scores or transcript didn't get to them right at the deadline (assuming the reason isn't just that you neglected to have them sent). You send them the unofficial versions so that they can evaluate you without having to wait for the official copies. Obviously they do need to get the official copies eventually though, or else you could have been lying.

I think it's important to keep in mind that schools are not looking for technicalities to reject qualified candidates. They want to get the best students they can.